This Project This web page originated as an assignment in Emory University's Biology 142 lab course. Students were assigned proteins of interest and asked to research what is known about the protein and to examine whether the newly sequenced whale shark genome had evidence of an orthologous protein. This specific Wiki page addresses IL18.
Background Information Interleukin-18 is a member of the IL-1 cytokine superfamily [5]. It is 196 amino acids long, and its function is to induce Th2-cytokines as part of an immune response [1]. The IL18 gene has been linked to inflammatory diseases such as Crohn's disease, atopic eczema, and asthma [6][7][8]. Figure 1 shows the structure of IL18 protein [9].
Figure 1: This is the structure of Interleukin-18 protein.
Figure 1: The structure of the Interleukin-18 protein.
Methods
The IL18 FASTA sequence was obtained using its ID (ENSP00000280357) through Ensembl[2]. The Georgia Aquarium Galaxy Server [3] was utilized to run a protein BLAST of the human protein sequence for IL18 as the query against the predicted whale shark protein database. The FASTA sequence was extracted for the top five chosen proteins. Each FASTA sequence was then BLASTed against the NCBI human protein database [1] to find the best match. The human sequence was the blasted against the mouse, zebra fish, yeast, clawed frog, dog, and elephant shark using the NCBI again to assess similarities across species. The FASTA sequences were extracted and Clustlaw [4] was used to form a phylogenic tree.
Whale shark protein research
The table in Figure 2 shows the results of blasting the human protein against the Georgia Aquarium whale shark database. We found a total of 8 whale shark genes in the search, and we narrowed down our results to the top five best matches using the most significant e-values and percent identities.
Figure 2: The data from blasting the humane IL18 protein against the whale shark genome. The top five results were chosen for our comparison based on the lowest e-values and the highest percent identities.
Protein domain The most likely ortholog in the whale shark protein database is the predicted interleukin-18 gene in the chimpanzee genome. It belongs to the IL-1 superfamily, just as the human gene does. The IL-1 family is a group of cytokines that serve their purpose during inflammation, a response of the immune system.
Comparing Species- Orthologs After blasting the human protein sequence for IL18 against whale shark, yeast, dog, zebra fish, mouse, clawed frog, and elephant genomes, no orthologs were found. However, when blasted against the chimpanzee genome, a predicted ortholog was found that seems to match exactly with the human IL18 gene, as shown in Figure 3. The fos-related antigen 2 gene was found in the whale shark, elephant shark, dog, clawed frog, zebra fish, and mouse genomes. This suggests that the species are marginally related by this gene.
Figure 3: This table is a compilation of the protein sequence information for the top five matching whale shark sequences as well as the most closely related protein sequences from a mouse, zebra fish, yeast, clawed frog, dog, elephant shark, and chimpanzee when blasted against the human protein sequence for IL18. Figure 4: A phylogenetic tree comparing the IL18 gene in humans to the most closely related gene in other species.
Conclusion The particular IL18 protein was only found in the chimpanzee genome. Based on the phylogenetic tree made specifically from protein sequences for the IL18 protein (shown in Figure 4), humans and chimpanzees are most closely related out of all of the genomes we observed.
We were unable to find a match for the human IL18 protein in whale sharks from the Georgia Aquarium database. More research is needed to determine how the interleukin-18 gene and the fos-related antigen 2 gene are related and how their functions are carried out in different organisms. It is possible that the gene was lost when the whale shark species diverged from the primate line. Further research could also discover the function of the fos-related antigen 2 gene, what proteins it could code for, and how these proteins act in the body of each organism. It is possible that the fos-related antigen 2 gene also codes for inflammatory responses in the immune systems of different organisms.
Gracie, J. Alistair, Susan E. Robertson, and Ian B. McInnes. "Interleukin-18."Journal of Leukocyte Biology 73.2 (2003): 213-24. Web. 11 Apr. 2015. <http://www.jleukbio.org/content/73/2/213.full>.
Novak, Natalija, Susanne Kruse, Jana Potreck, Laura Maintz, Claudia Jenneck, Stephan Weidinger, Rolf Fimmers, and Thomas Bieber. "Single Nucleotide Polymorphisms of the IL18 Gene Are Associated with Atopic Eczema." Journal of Allergy and Clinical Immunology 115.4 (2005): 828-33. Web. 28 Mar. 2015. <http://www.sciencedirect.com/science/article/pii/S009167490500151X>.
Shin, H. D., L. H. Kim, B. L. Park, Y. H. Choi, H.-S. Park, S.-J. Hong, B. W. Choi, J. H. Lee, and C.-S. Park. "Association of Interleukin 18 (IL18) Polymorphisms with Specific IgE Levels to Mite Allergens among Asthmatic Patients." Allergy 60.7 (2005): 900-06. Web. 28 Mar. 2015. <http://onlinelibrary.wiley.com/doi/10.1111/j.1398-9995.2005.00619.x/full>.
Tamura, Kazuo. "IL18 Polymorphism Is Associated with an Increased Risk of Crohn’s Disease." Journal of Gastroenterology 37.14 (2002): 111-16. Web. 28 Mar. 2015. <http://link.springer.com/article/10.1007/BF03326428#>.
Ashley Graham, Sabrina Madni, Kavita Athalye
This Project
This web page originated as an assignment in Emory University's Biology 142 lab course. Students were assigned proteins of interest and asked to research what is known about the protein and to examine whether the newly sequenced whale shark genome had evidence of an orthologous protein. This specific Wiki page addresses IL18.
Background Information
Interleukin-18 is a member of the IL-1 cytokine superfamily [5]. It is 196 amino acids long, and its function is to induce Th2-cytokines as part of an immune response [1]. The IL18 gene has been linked to inflammatory diseases such as Crohn's disease, atopic eczema, and asthma [6][7][8]. Figure 1 shows the structure of IL18 protein [9].
Figure 1: The structure of the Interleukin-18 protein.
Methods
The IL18 FASTA sequence was obtained using its ID (ENSP00000280357) through Ensembl[2]. The Georgia Aquarium Galaxy Server [3] was utilized to run a protein BLAST of the human protein sequence for IL18 as the query against the predicted whale shark protein database. The FASTA sequence was extracted for the top five chosen proteins. Each FASTA sequence was then BLASTed against the NCBI human protein database [1] to find the best match. The human sequence was the blasted against the mouse, zebra fish, yeast, clawed frog, dog, and elephant shark using the NCBI again to assess similarities across species. The FASTA sequences were extracted and Clustlaw [4] was used to form a phylogenic tree.
Whale shark protein research
The table in Figure 2 shows the results of blasting the human protein against the Georgia Aquarium whale shark database. We found a total of 8 whale shark genes in the search, and we narrowed down our results to the top five best matches using the most significant e-values and percent identities.
Figure 2: The data from blasting the humane IL18 protein against the whale shark genome. The top five results were chosen for our comparison based on the lowest e-values and the highest percent identities.
Protein domain
The most likely ortholog in the whale shark protein database is the predicted interleukin-18 gene in the chimpanzee genome. It belongs to the IL-1 superfamily, just as the human gene does. The IL-1 family is a group of cytokines that serve their purpose during inflammation, a response of the immune system.
Comparing Species- Orthologs
After blasting the human protein sequence for IL18 against whale shark, yeast, dog, zebra fish, mouse, clawed frog, and elephant genomes, no orthologs were found. However, when blasted against the chimpanzee genome, a predicted ortholog was found that seems to match exactly with the human IL18 gene, as shown in Figure 3. The fos-related antigen 2 gene was found in the whale shark, elephant shark, dog, clawed frog, zebra fish, and mouse genomes. This suggests that the species are marginally related by this gene.
Figure 3: This table is a compilation of the protein sequence information for the top five matching whale shark sequences as well as the most closely related protein sequences from a mouse, zebra fish, yeast, clawed frog, dog, elephant shark, and chimpanzee when blasted against the human protein sequence for IL18.
Figure 4: A phylogenetic tree comparing the IL18 gene in humans to the most closely related gene in other species.
Conclusion
The particular IL18 protein was only found in the chimpanzee genome. Based on the phylogenetic tree made specifically from protein sequences for the IL18 protein (shown in Figure 4), humans and chimpanzees are most closely related out of all of the genomes we observed.
We were unable to find a match for the human IL18 protein in whale sharks from the Georgia Aquarium database. More research is needed to determine how the interleukin-18 gene and the fos-related antigen 2 gene are related and how their functions are carried out in different organisms. It is possible that the gene was lost when the whale shark species diverged from the primate line. Further research could also discover the function of the fos-related antigen 2 gene, what proteins it could code for, and how these proteins act in the body of each organism. It is possible that the fos-related antigen 2 gene also codes for inflammatory responses in the immune systems of different organisms.
References